rs10104038

Variant names:

• chr8-42673886-G-C
• rs10104038

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0537 in 152,196 control chromosomes in the GnomAD database, including 275 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.054 (275 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.267
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0816 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0536 AC: 8153 AN: 152076 Hom.: 273 Cov.: 32

Gnomad AFR AF: 0.0835

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.0355

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0886

Gnomad FIN AF: 0.0497

Gnomad MID AF: 0.122

Gnomad NFE AF: 0.0386

Gnomad OTH AF: 0.0531

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0537 AC: 8170 AN: 152196 Hom.: 275 Cov.: 32 AF XY: 0.0541 AC XY: 4022 AN XY: 74412

African (AFR) AF: 0.0839 AC: 3484 AN: 41502

American (AMR) AF: 0.0354 AC: 542 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.102 AC: 353 AN: 3472

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5186

South Asian (SAS) AF: 0.0885 AC: 426 AN: 4816

European-Finnish (FIN) AF: 0.0497 AC: 527 AN: 10606

Middle Eastern (MID) AF: 0.106 AC: 31 AN: 292

European-Non Finnish (NFE) AF: 0.0386 AC: 2625 AN: 68006

Other (OTH) AF: 0.0521 AC: 110 AN: 2112

Alfa AF: 0.0469 Hom.: 21

Bravo AF: 0.0533

Asia WGS AF: 0.0390 AC: 137 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.3
DANN	Benign	0.28
PhyloP100		-0.27

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10104038; hg19: chr8-42529029;